Publish normalized and hvg scaled output results

vib-singlecell-nf · May 7, 2020 · 86d1456 · 86d1456
1 parent 56bddfd
commit 86d1456
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Showing 2 changed files with 14 additions and 5 deletions.
diff --git a/workflows/hvg_selection.nf b/workflows/hvg_selection.nf
@@ -3,7 +3,7 @@ nextflow.preview.dsl=2
 //////////////////////////////////////////////////////
 //  process imports:
 // utils
-include PUBLISH as PUBLISH_H5AD_HVG from "../../utils/workflows/utils.nf" params(params)
+include PUBLISH as PUBLISH_H5AD_HVG_SCALED from "../../utils/workflows/utils.nf" params(params)
 
 // scanpy:
 include SC__SCANPY__FIND_HIGHLY_VARIABLE_GENES from '../processes/feature_selection.nf' params(params)
@@ -25,13 +25,13 @@ workflow HVG_SELECTION {
         hvg = data \
             | SC__SCANPY__FIND_HIGHLY_VARIABLE_GENES \
             | SC__SCANPY__SUBSET_HIGHLY_VARIABLE_GENES
-        PUBLISH_H5AD_HVG(
-            SC__SCANPY__FIND_HIGHLY_VARIABLE_GENES.out,
-            null,
+        scaled = SC__SCANPY__FEATURE_SCALING( hvg )
+        PUBLISH_H5AD_HVG_SCALED(
+            scaled,
+            "SCANPY.hvg_scaled_output",
             "scanpy",
             false
         )
-        scaled = SC__SCANPY__FEATURE_SCALING( hvg )
         report = GENERATE_REPORT(
             "HVG",
             SC__SCANPY__FIND_HIGHLY_VARIABLE_GENES.out,

diff --git a/workflows/normalize_transform.nf b/workflows/normalize_transform.nf
@@ -2,6 +2,9 @@ nextflow.preview.dsl=2
 
 //////////////////////////////////////////////////////
 //  process imports:
+// utils
+include PUBLISH as PUBLISH_H5AD_NORMALIZED from "../../utils/workflows/utils.nf" params(params)
+
 
 // scanpy:
 include SC__SCANPY__DATA_TRANSFORMATION from '../processes/transform.nf' params(params)
@@ -16,6 +19,12 @@ workflow NORMALIZE_TRANSFORM {
 
     main:
         SC__SCANPY__NORMALIZATION( filtered )
+        PUBLISH_H5AD_NORMALIZED(
+            SC__SCANPY__NORMALIZATION.out,
+            "SCANPY.normalized_output",
+            "scanpy",
+            false
+        )
         SC__SCANPY__DATA_TRANSFORMATION( SC__SCANPY__NORMALIZATION.out )
 
     emit: